Hi Trevor,
On Thu, Sep 16, 2010 at 2:12 PM, Trevor Gokey <tgokey.mail.sfsu.edu> wrote:
> Hello,
>
> Is there any chance to have netCDF trajectory support for mmpbsa.py? I
> tried just adding netcdf to all the ptraj output, but since the final sander
> command gets sent to utils.py, I can't add the ioutfm=1 line in there.
> Sander is oh so much faster when reading binary.
>
I don't think we're going to add this. Ultimately we're going to move over
to NAB I think, when NAB gains the required functionality (decomposition)
and nab doesn't support netCDF. Also, the alanine scanning portion requires
ASCII crd files to operate. Lastly, how long is the trajectory reading
compared to the actual calculation? Does the entire trajectory file have to
get read in each time just to pull out one set of coordinate files (which
would be massively inefficient) or does it just read them as they need
them? You can add "ioutfm=1" to the gbmdin and pbmdin functions in utils.py
if you want, and then add the "netcdf" keyword at the end of the ptraj
output files in MMPBSA.py. However, we didn't really think the performance
increase of using netcdf warranted inclusion (since if coordinate reading is
the RDS, then it's pretty fast anyway ;) ).
> General question: how are the total energies calculated for the pb method?
> Gb looks straightforward because everything needed to calculate the total
> energy is listed in the final mmpbsa.py output. As for pb... an energy term
> that is used to calculate the final energy is missing from the total, or
> mmpbsa and I disagree on how to do general floating point arithmetic.
>
It's done in the same way that GB is. However, depending on your
"verbosity" setting, you can avoid printing a lot of redundant data. For
instance, for single-trajectory simulations, the bonded terms (including 1-4
interactions) must cancel or something has gone wrong. Therefore, they are
not printed by default (but they ARE checked for consistency and printed if
inconsistent). If they're not printed, they're subtracted from the reported
total. Only by setting verbose=2 in the input file will give you complete
agreement between the _MMPBSA_complex/receptor/ligand_pb.mdout files and the
final output file. Furthermore, G gas is the sum of the gas-phase terms
(VDWAALS, EEL, and the bonded terms if they're included) and G solv is the
sum of the solution phase terms (EPB and ECAVITY or EGB and ESURF for pb/gb,
respectively). Thus, all of the terms that come before the "total" should
add up to exactly twice the total, since that's what's added together. I
just checked it for amber11 by running the test files.
Hope this helps,
Jason
>
> Thank you,
> Trevor Gokey
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 16 2010 - 12:00:03 PDT
